Mercurial > repos > saket-choudhary > inchlib_clust
comparison inchlib_clust/inchlib_clust.xml @ 0:60f93f839759 draft default tip
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author | saket-choudhary |
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date | Tue, 07 Oct 2014 19:35:50 -0400 |
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-1:000000000000 | 0:60f93f839759 |
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1 <tool id="inchlib_clust" name="INCHlib" version="1.0.0" hidden="false"> | |
2 <requirements> | |
3 <requirement type="package" version="3.5.0">blas</requirement> | |
4 <requirement type="package" version="1.7">numpy</requirement> | |
5 <requirement type="package" version="0.12">scipy</requirement> | |
6 <requirement type="package" version="0.15">scikit-learn</requirement> | |
7 <requirement type="package" version="1.1.13">fastcluster</requirement> | |
8 <requirement type="python-module">numpy</requirement> | |
9 <requirement type="python-module">scipy</requirement> | |
10 <requirement type="python-module">scikit-learn</requirement> | |
11 <requirement type="python-module">fastcluster</requirement> | |
12 </requirements> | |
13 <description>Performs data clustering for input to InCHlib.js</description> | |
14 <command interpreter="python"> | |
15 inchlib_clust.py $input -o $output | |
16 --row_distance $row_distance | |
17 --row_linkage $row_linkage | |
18 --column_distance $column_distance | |
19 --column_linkage $column_linkage | |
20 --axis $axis | |
21 --datatype $datatype | |
22 --data_delimiter $data_delimiter | |
23 #if $data_header.data_header_present == "yes" | |
24 --data_header | |
25 #end if | |
26 #if $metadata_option.metadata_present == "yes" | |
27 --metadata $metadata_option.metadata | |
28 --metadata_delimiter $metadata_option.metadata_delimiter | |
29 #if $metadata_option.metadata_header.metadata_header_present == "yes" | |
30 --metadata_header | |
31 #end if | |
32 #if $metadata_option.metadata_compress_option.should_compress_metadata == "yes" | |
33 --metadata_compressed_value $metadata_option.metadata_compressed_value | |
34 #end if | |
35 #end if | |
36 #if $data_compress_option.should_compress_data == "yes" | |
37 --data_compressed_value $data_compressed_value | |
38 #end if | |
39 #if $should_normalize == "yes" | |
40 --normalize | |
41 #end if | |
42 </command> | |
43 <inputs> | |
44 <param format="text" name="input" type="data" label="Input File" /> | |
45 | |
46 <param name="row_distance" type="select" label="Row Distance Method" help="Set the distance to use for clustering rows"> | |
47 <option value="braycurtis">braycurtis</option> | |
48 <option value="canberra">canberra</option> | |
49 <option value="chebyshev">chebyshev</option> | |
50 <option value="cityblock">cityblock</option> | |
51 <option value="correlation">correlation</option> | |
52 <option value="cosine">cosine</option> | |
53 <option value="euclidean" selected="true">euclidean</option> | |
54 <option value="mahalanobis">mahalanobis</option> | |
55 <option value="minkowski">minkowski</option> | |
56 <option value="seuclidean">seuclidean</option> | |
57 <option value="sqeuclidean">sqeuclidean</option> | |
58 | |
59 <option value="dice">dice</option> | |
60 <option value="hamming">hamming</option> | |
61 <option value="jaccard">jaccard</option> | |
62 <option value="kulsinski">kulsinski</option> | |
63 <option value="matching">matching</option> | |
64 <option value="rogerstanimoto">rogerstanimoto</option> | |
65 <option value="russellrao">russellrao</option> | |
66 <option value="sokalmichener">sokalmichener</option> | |
67 <option value="sokalsneath">sokalsneath</option> | |
68 <option value="yule">yule</option> | |
69 </param> | |
70 | |
71 <param name="row_linkage" type="select" label="Row Linkage Method" help="Set the linkage to use for clustering rows"> | |
72 <option value="single">single</option> | |
73 <option value="complete">complete</option> | |
74 <option value="average">average</option> | |
75 <option value="centroid">centroid</option> | |
76 <option value="ward">ward</option> | |
77 <option value="median">median</option> | |
78 <option value="weighted">weighted</option> | |
79 | |
80 <option value="ward" selected="true">ward</option> | |
81 <option value="centroid">centroid</option> | |
82 </param> | |
83 | |
84 <param name="column_distance" type="select" label="Column Distance Method" help="Set the distance to use for clustering columns"> | |
85 <option value="braycurtis">braycurtis</option> | |
86 <option value="canberra">canberra</option> | |
87 <option value="chebyshev">chebyshev</option> | |
88 <option value="cityblock">cityblock</option> | |
89 <option value="correlation">correlation</option> | |
90 <option value="cosine">cosine</option> | |
91 <option value="euclidean" selected="true">euclidean</option> | |
92 <option value="mahalanobis">mahalanobis</option> | |
93 <option value="minkowski">minkowski</option> | |
94 <option value="seuclidean">seuclidean</option> | |
95 <option value="sqeuclidean">sqeuclidean</option> | |
96 | |
97 <option value="dice">dice</option> | |
98 <option value="hamming">hamming</option> | |
99 <option value="jaccard">jaccard</option> | |
100 <option value="kulsinski">kulsinski</option> | |
101 <option value="matching">matching</option> | |
102 <option value="rogerstanimoto">rogerstanimoto</option> | |
103 <option value="russellrao">russellrao</option> | |
104 <option value="sokalmichener">sokalmichener</option> | |
105 <option value="sokalsneath">sokalsneath</option> | |
106 <option value="yule">yule</option> | |
107 </param> | |
108 | |
109 <param name="column_linkage" type="select" label="Column Linkage" help="Set the linkage to use for clustering columns"> | |
110 <option value="single">single</option> | |
111 <option value="complete">complete</option> | |
112 <option value="average">average</option> | |
113 <option value="centroid">centroid</option> | |
114 <option value="ward">ward</option> | |
115 <option value="median">median</option> | |
116 <option value="weighted">weighted</option> | |
117 | |
118 <option value="ward" selected="true">ward</option> | |
119 <option value="centroid">centroid</option> | |
120 </param> | |
121 | |
122 <param name="axis" type="select" label="Clustering Axis"> | |
123 <option value="row" selected="true">row</option> | |
124 <option value="both">both</option> | |
125 </param> | |
126 | |
127 <param name="datatype" type="select" label="Type Of Data"> | |
128 <option value="numeric" selected="true">numeric</option> | |
129 <option value="binary">binary</option> | |
130 </param> | |
131 | |
132 <param name="data_delimiter" type="select" label="Data Delimiter"> | |
133 <option value="\t">tab</option> | |
134 <option value=",">comma</option> | |
135 <option value=";">semicolon</option> | |
136 </param> | |
137 | |
138 <conditional name="data_header"> | |
139 <param name="data_header_present" type="select" label="First row of file is header"> | |
140 <option value="yes">Yes</option> | |
141 <option value="no" selected="true">No</option> | |
142 </param> | |
143 </conditional> | |
144 | |
145 <conditional name="data_compress_option"> | |
146 <param name="should_compress_data" type="select" label="Compress Rows"> | |
147 <option value="yes">Yes</option> | |
148 <option value="no" selected="true">No</option> | |
149 </param> | |
150 <when value="yes"> | |
151 <param name="data_compressed_value" type="select"> | |
152 <option value="median" selected="true">median</option> | |
153 <option value="mean">mean</option> | |
154 </param> | |
155 </when> | |
156 </conditional> | |
157 | |
158 <param name="should_normalize" type="select" label="Normalise"> | |
159 <option value="yes">Yes</option> | |
160 <option value="no" selected="true">No</option> | |
161 </param> | |
162 | |
163 <conditional name="metadata_option"> | |
164 <param name="metadata_present" type="select" label="Metadata Input"> | |
165 <option value="yes">Yes</option> | |
166 <option value="no" selected="true">No</option> | |
167 </param> | |
168 <when value="yes"> | |
169 <param name="metadata" type="data" format="text" label="Metadata File"/> | |
170 <conditional name="metadata_header"> | |
171 <param name="metadata_header_present" type="select" label="Metadata Header Present?"> | |
172 <option value="yes">Yes</option> | |
173 <option value="no" selected="true">No</option> | |
174 </param> | |
175 </conditional> | |
176 <param name="metadata_delimiter" type="select" label="Metadata Delimiter"> | |
177 <option value="\t">tab</option> | |
178 <option value=",">comma</option> | |
179 <option value=";">semicolon</option> | |
180 </param> | |
181 <conditional name="metadata_compress_option"> | |
182 <param name="should_compress_metadata" type="select" label="Compress Metadata Rows?"> | |
183 <option value="yes">Yes</option> | |
184 <option value="no" selected="true">No</option> | |
185 </param> | |
186 <when value="yes"> | |
187 <param name="metadata_compressed_value" type="select"> | |
188 <option value="median" selected="true">median</option> | |
189 <option value="mean">mean</option> | |
190 <option value="frequency">frequency</option> | |
191 </param> | |
192 </when> | |
193 </conditional> | |
194 </when> | |
195 </conditional> | |
196 </inputs> | |
197 | |
198 <outputs> | |
199 <data format="json" name="output" label="${tool.name} on ${on_string}: output" /> | |
200 </outputs> | |
201 | |
202 <tests> | |
203 <test> | |
204 <param name="input" value="inchlib_input1.csv"/> | |
205 <param name="row_distance" value="euclidean"/> | |
206 <param name="row_linkage" value="ward"/> | |
207 <param name="column_distance" value="euclidean"/> | |
208 <param name="column_linkage" value="ward"/> | |
209 <param name="axis" value="row" /> | |
210 <param name="datatype" value="numeric" /> | |
211 <param name="data_delimiter" value="," /> | |
212 <param name="data_header_present" value="yes" /> | |
213 <param name="should_compress_data" value="no" /> | |
214 <param name="should_normalize" value="no" /> | |
215 <param name="metadata_present" value="yes" /> | |
216 <param name="metadata" value="inchlib_input_metadata.csv" /> | |
217 <param name="metadata_delimiter" value="," /> | |
218 <param name="metadata_header_present" value="yes" /> | |
219 <output name="output" file="inchlib_output.json" ftype="json" /> | |
220 </test> | |
221 </tests> | |
222 | |
223 <help> | |
224 **What it does** | |
225 | |
226 Performs data clustering and prepares input data for InCHlib. | |
227 | |
228 | |
229 </help> | |
230 </tool> |